Starting phenix.real_space_refine on Sun May 18 17:50:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x8l_38148/05_2025/8x8l_38148.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x8l_38148/05_2025/8x8l_38148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x8l_38148/05_2025/8x8l_38148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x8l_38148/05_2025/8x8l_38148.map" model { file = "/net/cci-nas-00/data/ceres_data/8x8l_38148/05_2025/8x8l_38148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x8l_38148/05_2025/8x8l_38148.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 59 5.16 5 C 5641 2.51 5 N 1531 2.21 5 O 1620 1.98 5 H 8704 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17555 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3854 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 1 Chain: "B" Number of atoms: 4996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 4996 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 200 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "E" Number of atoms: 3385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3385 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 834 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 4286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 4286 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 14, 'TRANS': 257} Chain breaks: 1 Time building chain proxies: 8.31, per 1000 atoms: 0.47 Number of scatterers: 17555 At special positions: 0 Unit cell: (123.6, 93.936, 129.368, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 59 16.00 O 1620 8.00 N 1531 7.00 C 5641 6.00 H 8704 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 154 " distance=2.03 Simple disulfide: pdb=" SG CYS C 5 " - pdb=" SG CYS C 16 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 112 " - pdb=" SG CYS R 186 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.55 Conformation dependent library (CDL) restraints added in 1.5 seconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2130 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 14 sheets defined 39.2% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.518A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 44 Processing helix chain 'A' and resid 45 through 51 removed outlier: 3.715A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.625A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 245 removed outlier: 4.506A pdb=" N GLN A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLU A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 250 removed outlier: 4.092A pdb=" N ARG A 250 " --> pdb=" O ARG A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.627A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 279 through 285 removed outlier: 3.608A pdb=" N TYR A 285 " --> pdb=" O PHE A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 319 removed outlier: 3.792A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 12 through 30 Processing helix chain 'B' and resid 34 through 40 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.540A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 23 removed outlier: 3.571A pdb=" N ASN G 23 " --> pdb=" O LYS G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 43 Processing helix chain 'R' and resid 43 through 67 Processing helix chain 'R' and resid 73 through 91 Processing helix chain 'R' and resid 92 through 102 removed outlier: 3.578A pdb=" N ALA R 102 " --> pdb=" O THR R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 143 removed outlier: 4.346A pdb=" N LEU R 111 " --> pdb=" O PHE R 107 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU R 114 " --> pdb=" O VAL R 110 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET R 116 " --> pdb=" O CYS R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 178 Proline residue: R 173 - end of helix Processing helix chain 'R' and resid 180 through 184 removed outlier: 4.438A pdb=" N GLY R 183 " --> pdb=" O VAL R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 210 Processing helix chain 'R' and resid 210 through 235 Processing helix chain 'R' and resid 241 through 274 Proline residue: R 263 - end of helix Processing helix chain 'R' and resid 282 through 304 removed outlier: 4.188A pdb=" N TYR R 286 " --> pdb=" O SER R 282 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE R 287 " --> pdb=" O ALA R 283 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN R 296 " --> pdb=" O LEU R 292 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER R 297 " --> pdb=" O SER R 293 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 308 through 316 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 4.662A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 57 removed outlier: 6.037A pdb=" N THR B 52 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASN B 345 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG B 54 " --> pdb=" O ILE B 343 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N PHE B 340 " --> pdb=" O SER B 336 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS B 322 " --> pdb=" O GLY B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.644A pdb=" N ILE B 85 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER B 79 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU B 84 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA B 97 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE B 86 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.618A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE B 128 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG B 139 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156 removed outlier: 3.871A pdb=" N THR B 183 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197 removed outlier: 6.643A pdb=" N GLY B 207 " --> pdb=" O MET B 193 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU B 195 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B 205 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LEU B 197 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU B 203 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER B 206 " --> pdb=" O LYS B 214 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS B 214 " --> pdb=" O SER B 206 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 3.542A pdb=" N MET B 267 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLU B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 4.054A pdb=" N SER B 280 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 6 through 8 Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.566A pdb=" N SER E 71 " --> pdb=" O PHE E 80 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.952A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.573A pdb=" N VAL E 155 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 194 through 195 removed outlier: 6.519A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN E 231 " --> pdb=" O THR E 238 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 194 through 195 removed outlier: 6.519A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) 460 hydrogen bonds defined for protein. 1278 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.04 Time building geometry restraints manager: 5.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 8678 1.02 - 1.22: 46 1.22 - 1.42: 3825 1.42 - 1.62: 5112 1.62 - 1.82: 84 Bond restraints: 17745 Sorted by residual: bond pdb=" SG CYS R 260 " pdb=" HG CYS R 260 " ideal model delta sigma weight residual 1.200 1.339 -0.139 2.00e-02 2.50e+03 4.86e+01 bond pdb=" ND2 ASN R 310 " pdb="HD22 ASN R 310 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.57e+01 bond pdb=" ND2 ASN R 310 " pdb="HD21 ASN R 310 " ideal model delta sigma weight residual 0.860 0.979 -0.119 2.00e-02 2.50e+03 3.57e+01 bond pdb=" NE ARG R 312 " pdb=" HE ARG R 312 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" NE ARG A 309 " pdb=" HE ARG A 309 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.02e+01 ... (remaining 17740 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.78: 31897 7.78 - 15.56: 4 15.56 - 23.33: 0 23.33 - 31.11: 1 31.11 - 38.89: 2 Bond angle restraints: 31904 Sorted by residual: angle pdb=" C PRO G 54 " pdb=" CA PRO G 54 " pdb=" HA PRO G 54 " ideal model delta sigma weight residual 109.00 70.11 38.89 3.00e+00 1.11e-01 1.68e+02 angle pdb=" N PRO G 54 " pdb=" CA PRO G 54 " pdb=" HA PRO G 54 " ideal model delta sigma weight residual 110.00 74.57 35.43 3.00e+00 1.11e-01 1.39e+02 angle pdb=" CB PRO G 54 " pdb=" CA PRO G 54 " pdb=" HA PRO G 54 " ideal model delta sigma weight residual 109.00 78.81 30.19 3.00e+00 1.11e-01 1.01e+02 angle pdb=" N VAL R 207 " pdb=" CA VAL R 207 " pdb=" C VAL R 207 " ideal model delta sigma weight residual 110.30 117.07 -6.77 9.70e-01 1.06e+00 4.87e+01 angle pdb=" N SER A 228 " pdb=" CA SER A 228 " pdb=" C SER A 228 " ideal model delta sigma weight residual 111.82 119.15 -7.33 1.16e+00 7.43e-01 3.99e+01 ... (remaining 31899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 7798 17.74 - 35.49: 395 35.49 - 53.23: 168 53.23 - 70.97: 47 70.97 - 88.72: 9 Dihedral angle restraints: 8417 sinusoidal: 4475 harmonic: 3942 Sorted by residual: dihedral pdb=" CB CYS R 112 " pdb=" SG CYS R 112 " pdb=" SG CYS R 186 " pdb=" CB CYS R 186 " ideal model delta sinusoidal sigma weight residual -86.00 -137.94 51.94 1 1.00e+01 1.00e-02 3.68e+01 dihedral pdb=" C PHE R 211 " pdb=" N PHE R 211 " pdb=" CA PHE R 211 " pdb=" CB PHE R 211 " ideal model delta harmonic sigma weight residual -122.60 -134.21 11.61 0 2.50e+00 1.60e-01 2.16e+01 dihedral pdb=" N PRO G 54 " pdb=" C PRO G 54 " pdb=" CA PRO G 54 " pdb=" CB PRO G 54 " ideal model delta harmonic sigma weight residual 115.10 124.31 -9.21 0 2.50e+00 1.60e-01 1.36e+01 ... (remaining 8414 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1299 0.095 - 0.190: 87 0.190 - 0.286: 7 0.286 - 0.381: 1 0.381 - 0.476: 3 Chirality restraints: 1397 Sorted by residual: chirality pdb=" CA PRO G 54 " pdb=" N PRO G 54 " pdb=" C PRO G 54 " pdb=" CB PRO G 54 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.48 2.00e-01 2.50e+01 5.66e+00 chirality pdb=" CA PHE R 211 " pdb=" N PHE R 211 " pdb=" C PHE R 211 " pdb=" CB PHE R 211 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.90e+00 chirality pdb=" CA CYS R 260 " pdb=" N CYS R 260 " pdb=" C CYS R 260 " pdb=" CB CYS R 260 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.70e+00 ... (remaining 1394 not shown) Planarity restraints: 2649 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN R 313 " -0.112 2.00e-02 2.50e+03 1.24e-01 2.31e+02 pdb=" CD GLN R 313 " 0.005 2.00e-02 2.50e+03 pdb=" OE1 GLN R 313 " 0.110 2.00e-02 2.50e+03 pdb=" NE2 GLN R 313 " -0.003 2.00e-02 2.50e+03 pdb="HE21 GLN R 313 " 0.184 2.00e-02 2.50e+03 pdb="HE22 GLN R 313 " -0.184 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN R 310 " -0.053 2.00e-02 2.50e+03 5.25e-02 4.14e+01 pdb=" CG ASN R 310 " 0.002 2.00e-02 2.50e+03 pdb=" OD1 ASN R 310 " 0.052 2.00e-02 2.50e+03 pdb=" ND2 ASN R 310 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN R 310 " 0.074 2.00e-02 2.50e+03 pdb="HD22 ASN R 310 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN R 316 " -0.017 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" N LYS R 317 " 0.056 2.00e-02 2.50e+03 pdb=" CA LYS R 317 " -0.014 2.00e-02 2.50e+03 pdb=" H LYS R 317 " -0.024 2.00e-02 2.50e+03 ... (remaining 2646 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 945 2.19 - 2.79: 35777 2.79 - 3.40: 48855 3.40 - 4.00: 63338 4.00 - 4.60: 97911 Nonbonded interactions: 246826 Sorted by model distance: nonbonded pdb=" O LYS G 19 " pdb="HD21 ASN G 23 " model vdw 1.590 2.450 nonbonded pdb="HH22 ARG A 208 " pdb=" OD1 ASP A 239 " model vdw 1.626 2.450 nonbonded pdb=" OE2 GLU A 8 " pdb=" HH TYR E 175 " model vdw 1.637 2.450 nonbonded pdb=" O ILE E 138 " pdb=" HG1 THR E 238 " model vdw 1.638 2.450 nonbonded pdb="HH12 ARG E 202 " pdb=" OD2 ASP E 223 " model vdw 1.640 2.450 ... (remaining 246821 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.320 Extract box with map and model: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 37.540 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9045 Z= 0.312 Angle : 0.603 9.479 12277 Z= 0.377 Chirality : 0.050 0.476 1397 Planarity : 0.003 0.034 1557 Dihedral : 9.651 75.047 3215 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.89 % Allowed : 3.68 % Favored : 94.43 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.26), residues: 1122 helix: 2.97 (0.27), residues: 385 sheet: 1.24 (0.32), residues: 268 loop : 0.15 (0.31), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP R 261 HIS 0.002 0.001 HIS A 329 PHE 0.015 0.001 PHE R 315 TYR 0.009 0.001 TYR R 89 ARG 0.004 0.000 ARG R 67 Details of bonding type rmsd hydrogen bonds : bond 0.20308 ( 449) hydrogen bonds : angle 6.67040 ( 1278) SS BOND : bond 0.00211 ( 4) SS BOND : angle 0.84928 ( 8) covalent geometry : bond 0.00436 ( 9041) covalent geometry : angle 0.60270 (12269) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 371 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 353 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 104 PHE cc_start: 0.5863 (t80) cc_final: 0.5513 (t80) REVERT: R 288 PHE cc_start: 0.7375 (t80) cc_final: 0.7130 (t80) REVERT: R 315 PHE cc_start: 0.7383 (t80) cc_final: 0.7085 (t80) outliers start: 18 outliers final: 5 residues processed: 363 average time/residue: 2.4395 time to fit residues: 946.2753 Evaluate side-chains 181 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 176 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 300 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 0.0000 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 204 GLN A 213 GLN A 234 GLN B 49 GLN B 225 GLN B 264 GLN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN R 81 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.145655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.117824 restraints weight = 38586.158| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.15 r_work: 0.3461 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9045 Z= 0.130 Angle : 0.543 8.626 12277 Z= 0.286 Chirality : 0.043 0.474 1397 Planarity : 0.005 0.062 1557 Dihedral : 5.039 74.997 1249 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.41 % Allowed : 18.91 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.26), residues: 1122 helix: 3.15 (0.26), residues: 385 sheet: 0.90 (0.31), residues: 255 loop : 0.31 (0.31), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 302 HIS 0.004 0.001 HIS B 59 PHE 0.012 0.001 PHE E 203 TYR 0.015 0.001 TYR R 63 ARG 0.006 0.001 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.04524 ( 449) hydrogen bonds : angle 5.00197 ( 1278) SS BOND : bond 0.00906 ( 4) SS BOND : angle 3.04818 ( 8) covalent geometry : bond 0.00283 ( 9041) covalent geometry : angle 0.53784 (12269) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 225 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 183 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASN cc_start: 0.7350 (m-40) cc_final: 0.7110 (m-40) REVERT: A 281 GLU cc_start: 0.8452 (mp0) cc_final: 0.8249 (mm-30) REVERT: B 50 MET cc_start: 0.8297 (mtm) cc_final: 0.8013 (mtm) REVERT: B 242 ASN cc_start: 0.7916 (p0) cc_final: 0.7285 (t160) REVERT: E 18 ARG cc_start: 0.7710 (tpp80) cc_final: 0.7434 (tpt-90) REVERT: E 87 ARG cc_start: 0.7231 (mtm-85) cc_final: 0.6872 (mtt90) REVERT: R 104 PHE cc_start: 0.6185 (t80) cc_final: 0.5627 (t80) REVERT: R 288 PHE cc_start: 0.7597 (t80) cc_final: 0.7151 (t80) REVERT: R 315 PHE cc_start: 0.7366 (t80) cc_final: 0.7101 (t80) outliers start: 42 outliers final: 15 residues processed: 211 average time/residue: 2.1666 time to fit residues: 492.5318 Evaluate side-chains 177 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 308 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 75 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 45 optimal weight: 0.0870 chunk 99 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 overall best weight: 2.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 GLN B 181 GLN B 264 GLN E 77 ASN G 17 GLN R 100 ASN R 296 ASN R 313 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.136748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.107382 restraints weight = 38646.344| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.14 r_work: 0.3309 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9045 Z= 0.190 Angle : 0.575 7.927 12277 Z= 0.311 Chirality : 0.044 0.430 1397 Planarity : 0.005 0.044 1557 Dihedral : 4.711 52.380 1245 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.10 % Allowed : 18.59 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.26), residues: 1122 helix: 2.79 (0.25), residues: 386 sheet: 0.54 (0.31), residues: 250 loop : -0.05 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 36 HIS 0.006 0.002 HIS B 230 PHE 0.018 0.002 PHE R 124 TYR 0.018 0.002 TYR R 294 ARG 0.005 0.001 ARG R 149 Details of bonding type rmsd hydrogen bonds : bond 0.04599 ( 449) hydrogen bonds : angle 4.88490 ( 1278) SS BOND : bond 0.01771 ( 4) SS BOND : angle 1.57795 ( 8) covalent geometry : bond 0.00429 ( 9041) covalent geometry : angle 0.57330 (12269) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 203 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 164 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.7327 (t0) cc_final: 0.7055 (t0) REVERT: A 231 ASN cc_start: 0.7908 (m-40) cc_final: 0.7662 (m110) REVERT: B 38 ILE cc_start: 0.8148 (tp) cc_final: 0.7898 (mm) REVERT: B 48 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.7863 (mp) REVERT: B 139 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7548 (ppt-90) REVERT: B 261 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.6625 (mtp85) REVERT: B 298 ASN cc_start: 0.8181 (p0) cc_final: 0.7977 (p0) REVERT: B 345 ASN cc_start: 0.7398 (t160) cc_final: 0.7178 (t0) REVERT: E 18 ARG cc_start: 0.7685 (tpp80) cc_final: 0.7276 (tpt-90) REVERT: E 87 ARG cc_start: 0.7167 (mtm-85) cc_final: 0.6789 (mtt90) REVERT: R 315 PHE cc_start: 0.7529 (t80) cc_final: 0.7204 (t80) outliers start: 39 outliers final: 20 residues processed: 194 average time/residue: 2.1173 time to fit residues: 443.3309 Evaluate side-chains 174 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 308 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 55 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 GLN B 345 ASN R 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.134299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.104707 restraints weight = 38804.721| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.16 r_work: 0.3268 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.5783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9045 Z= 0.216 Angle : 0.590 8.621 12277 Z= 0.316 Chirality : 0.045 0.427 1397 Planarity : 0.005 0.043 1557 Dihedral : 4.802 51.445 1243 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.10 % Allowed : 18.80 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.25), residues: 1122 helix: 2.48 (0.25), residues: 393 sheet: 0.31 (0.31), residues: 256 loop : -0.37 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 211 HIS 0.006 0.002 HIS A 324 PHE 0.014 0.002 PHE B 156 TYR 0.014 0.002 TYR R 294 ARG 0.004 0.001 ARG A 54 Details of bonding type rmsd hydrogen bonds : bond 0.04496 ( 449) hydrogen bonds : angle 4.89338 ( 1278) SS BOND : bond 0.01314 ( 4) SS BOND : angle 1.01290 ( 8) covalent geometry : bond 0.00494 ( 9041) covalent geometry : angle 0.58949 (12269) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 188 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.7322 (t0) cc_final: 0.7052 (t0) REVERT: A 284 ARG cc_start: 0.7501 (ptp90) cc_final: 0.7266 (ptt-90) REVERT: B 38 ILE cc_start: 0.8216 (tp) cc_final: 0.7927 (mm) REVERT: B 48 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.7960 (mp) REVERT: B 50 MET cc_start: 0.8423 (mtm) cc_final: 0.8066 (mtm) REVERT: B 139 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7670 (ppt-90) REVERT: B 261 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.6690 (mtp85) REVERT: B 263 ASP cc_start: 0.7605 (t0) cc_final: 0.7345 (t0) REVERT: E 18 ARG cc_start: 0.7473 (tpp80) cc_final: 0.7111 (tpt-90) REVERT: E 43 LYS cc_start: 0.8512 (mppt) cc_final: 0.8265 (mmtp) REVERT: G 37 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8066 (ttp) REVERT: R 315 PHE cc_start: 0.7564 (t80) cc_final: 0.7203 (t80) outliers start: 39 outliers final: 18 residues processed: 176 average time/residue: 2.1985 time to fit residues: 417.4079 Evaluate side-chains 157 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 245 LYS Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 308 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 49 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 77 optimal weight: 0.0060 chunk 62 optimal weight: 4.9990 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN B 49 GLN R 100 ASN R 143 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.134193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.104559 restraints weight = 38941.344| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.14 r_work: 0.3264 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.6012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9045 Z= 0.174 Angle : 0.555 8.198 12277 Z= 0.296 Chirality : 0.043 0.429 1397 Planarity : 0.004 0.048 1557 Dihedral : 4.636 50.180 1242 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.31 % Allowed : 18.80 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.25), residues: 1122 helix: 2.62 (0.25), residues: 387 sheet: 0.20 (0.32), residues: 255 loop : -0.35 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 211 HIS 0.004 0.001 HIS A 324 PHE 0.010 0.001 PHE B 156 TYR 0.012 0.001 TYR R 294 ARG 0.005 0.000 ARG R 113 Details of bonding type rmsd hydrogen bonds : bond 0.04276 ( 449) hydrogen bonds : angle 4.79302 ( 1278) SS BOND : bond 0.01255 ( 4) SS BOND : angle 1.05787 ( 8) covalent geometry : bond 0.00390 ( 9041) covalent geometry : angle 0.55421 (12269) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 141 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 ARG cc_start: 0.7475 (ptp90) cc_final: 0.7263 (ptt-90) REVERT: B 38 ILE cc_start: 0.8217 (tp) cc_final: 0.7933 (mm) REVERT: B 48 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.7983 (mp) REVERT: B 50 MET cc_start: 0.8508 (mtm) cc_final: 0.8119 (mtm) REVERT: B 139 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7690 (ppt-90) REVERT: B 239 PHE cc_start: 0.9013 (OUTLIER) cc_final: 0.8402 (m-80) REVERT: B 261 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.6656 (mtp85) REVERT: B 263 ASP cc_start: 0.7607 (t0) cc_final: 0.7312 (t0) REVERT: E 18 ARG cc_start: 0.7450 (tpp80) cc_final: 0.7050 (tpt-90) REVERT: E 43 LYS cc_start: 0.8485 (mppt) cc_final: 0.8213 (mmtp) REVERT: R 315 PHE cc_start: 0.7627 (t80) cc_final: 0.7262 (t80) REVERT: R 317 LYS cc_start: 0.5090 (mttt) cc_final: 0.4576 (mtmm) outliers start: 41 outliers final: 23 residues processed: 174 average time/residue: 2.1897 time to fit residues: 410.6667 Evaluate side-chains 154 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 266 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 63 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 42 optimal weight: 0.0870 chunk 80 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 96 optimal weight: 0.7980 overall best weight: 2.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN R 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.134188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.104541 restraints weight = 39031.333| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.14 r_work: 0.3266 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.6138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9045 Z= 0.164 Angle : 0.545 7.998 12277 Z= 0.291 Chirality : 0.043 0.428 1397 Planarity : 0.004 0.048 1557 Dihedral : 4.620 48.945 1242 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.10 % Allowed : 19.01 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.25), residues: 1122 helix: 2.62 (0.25), residues: 387 sheet: 0.14 (0.32), residues: 255 loop : -0.38 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 211 HIS 0.004 0.001 HIS B 230 PHE 0.011 0.001 PHE R 287 TYR 0.012 0.001 TYR R 204 ARG 0.004 0.000 ARG R 113 Details of bonding type rmsd hydrogen bonds : bond 0.04152 ( 449) hydrogen bonds : angle 4.75524 ( 1278) SS BOND : bond 0.01817 ( 4) SS BOND : angle 0.73690 ( 8) covalent geometry : bond 0.00369 ( 9041) covalent geometry : angle 0.54453 (12269) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 135 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 38 ILE cc_start: 0.8196 (tp) cc_final: 0.7867 (mm) REVERT: B 48 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.7982 (mp) REVERT: B 50 MET cc_start: 0.8484 (mtm) cc_final: 0.8120 (mtm) REVERT: B 139 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7653 (ppt-90) REVERT: B 239 PHE cc_start: 0.9007 (OUTLIER) cc_final: 0.8322 (m-80) REVERT: B 261 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.6642 (mtp85) REVERT: B 263 ASP cc_start: 0.7647 (t0) cc_final: 0.7358 (t0) REVERT: B 267 MET cc_start: 0.8116 (mtp) cc_final: 0.7906 (mtp) REVERT: E 18 ARG cc_start: 0.7465 (tpp80) cc_final: 0.7060 (tpt-90) REVERT: E 43 LYS cc_start: 0.8476 (mppt) cc_final: 0.8187 (mmtp) REVERT: R 249 MET cc_start: 0.8068 (tpp) cc_final: 0.7799 (tpp) REVERT: R 315 PHE cc_start: 0.7648 (t80) cc_final: 0.7286 (t80) REVERT: R 317 LYS cc_start: 0.4848 (mttt) cc_final: 0.4434 (mtmm) outliers start: 39 outliers final: 26 residues processed: 168 average time/residue: 2.2125 time to fit residues: 401.0104 Evaluate side-chains 156 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 245 LYS Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 308 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 16 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN B 18 GLN R 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.133832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.104167 restraints weight = 38934.071| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.14 r_work: 0.3260 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.6264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9045 Z= 0.174 Angle : 0.555 8.642 12277 Z= 0.296 Chirality : 0.043 0.428 1397 Planarity : 0.005 0.049 1557 Dihedral : 4.702 48.110 1242 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.83 % Allowed : 18.59 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.25), residues: 1122 helix: 2.47 (0.25), residues: 393 sheet: 0.15 (0.32), residues: 256 loop : -0.49 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 211 HIS 0.004 0.001 HIS B 230 PHE 0.013 0.001 PHE R 287 TYR 0.011 0.001 TYR R 204 ARG 0.004 0.000 ARG R 113 Details of bonding type rmsd hydrogen bonds : bond 0.04186 ( 449) hydrogen bonds : angle 4.73675 ( 1278) SS BOND : bond 0.01588 ( 4) SS BOND : angle 1.25868 ( 8) covalent geometry : bond 0.00391 ( 9041) covalent geometry : angle 0.55384 (12269) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 134 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 38 ILE cc_start: 0.8255 (tp) cc_final: 0.7911 (mm) REVERT: B 48 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8017 (mp) REVERT: B 139 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7693 (ppt-90) REVERT: B 219 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7373 (mtt180) REVERT: B 261 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.6582 (mtp85) REVERT: B 263 ASP cc_start: 0.7750 (t0) cc_final: 0.7438 (t0) REVERT: E 18 ARG cc_start: 0.7512 (tpp80) cc_final: 0.7091 (tpt-90) REVERT: E 43 LYS cc_start: 0.8480 (mppt) cc_final: 0.8173 (mmtp) REVERT: R 125 THR cc_start: 0.8758 (OUTLIER) cc_final: 0.8538 (t) REVERT: R 249 MET cc_start: 0.8088 (tpp) cc_final: 0.7812 (tpp) REVERT: R 315 PHE cc_start: 0.7645 (t80) cc_final: 0.7316 (t80) REVERT: R 317 LYS cc_start: 0.4956 (mttt) cc_final: 0.4474 (mtmm) outliers start: 46 outliers final: 29 residues processed: 171 average time/residue: 2.2737 time to fit residues: 417.9350 Evaluate side-chains 158 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 245 LYS Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 308 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 2 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN B 49 GLN R 100 ASN R 313 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.134480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.104977 restraints weight = 38652.981| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.14 r_work: 0.3274 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.6317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9045 Z= 0.138 Angle : 0.534 7.785 12277 Z= 0.283 Chirality : 0.043 0.430 1397 Planarity : 0.004 0.048 1557 Dihedral : 4.588 46.721 1242 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.15 % Allowed : 20.06 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.26), residues: 1122 helix: 2.72 (0.26), residues: 387 sheet: 0.23 (0.32), residues: 254 loop : -0.40 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 211 HIS 0.003 0.001 HIS B 230 PHE 0.012 0.001 PHE R 287 TYR 0.012 0.001 TYR R 89 ARG 0.003 0.000 ARG R 113 Details of bonding type rmsd hydrogen bonds : bond 0.03943 ( 449) hydrogen bonds : angle 4.64574 ( 1278) SS BOND : bond 0.01218 ( 4) SS BOND : angle 1.42600 ( 8) covalent geometry : bond 0.00309 ( 9041) covalent geometry : angle 0.53330 (12269) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 166 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 1.422 Fit side-chains revert: symmetry clash REVERT: A 229 ASP cc_start: 0.7305 (t0) cc_final: 0.7026 (t0) REVERT: B 38 ILE cc_start: 0.8237 (tp) cc_final: 0.7893 (mm) REVERT: B 48 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8006 (mp) REVERT: B 50 MET cc_start: 0.8496 (mtm) cc_final: 0.8085 (mtm) REVERT: B 261 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.6613 (mtp85) REVERT: B 263 ASP cc_start: 0.7750 (t0) cc_final: 0.7457 (t0) REVERT: E 18 ARG cc_start: 0.7543 (tpp80) cc_final: 0.7142 (tpt-90) REVERT: E 43 LYS cc_start: 0.8475 (mppt) cc_final: 0.8164 (mmtp) REVERT: R 125 THR cc_start: 0.8775 (OUTLIER) cc_final: 0.8550 (t) REVERT: R 315 PHE cc_start: 0.7641 (t80) cc_final: 0.7286 (t80) REVERT: R 317 LYS cc_start: 0.4950 (mttt) cc_final: 0.4453 (mtmm) outliers start: 30 outliers final: 23 residues processed: 160 average time/residue: 2.2775 time to fit residues: 392.1035 Evaluate side-chains 152 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 245 LYS Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 274 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 108 optimal weight: 0.0470 overall best weight: 1.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN B 49 GLN R 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.135324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.105850 restraints weight = 39058.205| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.14 r_work: 0.3287 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.6346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9045 Z= 0.118 Angle : 0.520 7.490 12277 Z= 0.273 Chirality : 0.042 0.433 1397 Planarity : 0.004 0.060 1557 Dihedral : 4.479 45.342 1242 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.47 % Allowed : 19.43 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.26), residues: 1122 helix: 2.85 (0.25), residues: 387 sheet: 0.17 (0.32), residues: 259 loop : -0.32 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 174 HIS 0.003 0.001 HIS B 230 PHE 0.014 0.001 PHE R 287 TYR 0.011 0.001 TYR R 89 ARG 0.010 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 449) hydrogen bonds : angle 4.55582 ( 1278) SS BOND : bond 0.00922 ( 4) SS BOND : angle 1.11531 ( 8) covalent geometry : bond 0.00264 ( 9041) covalent geometry : angle 0.51934 (12269) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.7349 (t0) cc_final: 0.7048 (t0) REVERT: B 38 ILE cc_start: 0.8254 (tp) cc_final: 0.7924 (mm) REVERT: B 48 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8004 (mp) REVERT: B 50 MET cc_start: 0.8493 (mtm) cc_final: 0.8072 (mtm) REVERT: B 239 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.8279 (m-80) REVERT: B 263 ASP cc_start: 0.7757 (t0) cc_final: 0.7525 (t0) REVERT: E 18 ARG cc_start: 0.7553 (tpp80) cc_final: 0.7121 (tpt-90) REVERT: E 43 LYS cc_start: 0.8473 (mppt) cc_final: 0.8166 (mmtp) REVERT: E 87 ARG cc_start: 0.7019 (mtm-85) cc_final: 0.6402 (ptt-90) REVERT: R 125 THR cc_start: 0.8772 (OUTLIER) cc_final: 0.8551 (t) REVERT: R 249 MET cc_start: 0.8076 (tpp) cc_final: 0.7839 (tpp) REVERT: R 315 PHE cc_start: 0.7639 (t80) cc_final: 0.7303 (t80) REVERT: R 317 LYS cc_start: 0.4944 (mttt) cc_final: 0.4434 (mtmm) outliers start: 33 outliers final: 25 residues processed: 160 average time/residue: 2.0769 time to fit residues: 359.5329 Evaluate side-chains 158 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 274 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 54 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN R 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.135921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.106582 restraints weight = 38642.590| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.14 r_work: 0.3296 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.6348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9045 Z= 0.111 Angle : 0.515 7.091 12277 Z= 0.270 Chirality : 0.042 0.436 1397 Planarity : 0.005 0.055 1557 Dihedral : 4.383 43.675 1242 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.63 % Allowed : 20.80 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.26), residues: 1122 helix: 2.94 (0.26), residues: 387 sheet: 0.26 (0.32), residues: 266 loop : -0.25 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 174 HIS 0.003 0.001 HIS B 230 PHE 0.013 0.001 PHE R 287 TYR 0.010 0.001 TYR R 89 ARG 0.008 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03622 ( 449) hydrogen bonds : angle 4.49361 ( 1278) SS BOND : bond 0.01038 ( 4) SS BOND : angle 1.09193 ( 8) covalent geometry : bond 0.00246 ( 9041) covalent geometry : angle 0.51457 (12269) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 38 ILE cc_start: 0.8251 (tp) cc_final: 0.7920 (mm) REVERT: B 48 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.7986 (mp) REVERT: B 50 MET cc_start: 0.8464 (mtm) cc_final: 0.8040 (mtm) REVERT: B 170 THR cc_start: 0.8773 (p) cc_final: 0.8543 (p) REVERT: B 239 PHE cc_start: 0.8969 (OUTLIER) cc_final: 0.8276 (m-80) REVERT: B 263 ASP cc_start: 0.7746 (t0) cc_final: 0.7517 (t0) REVERT: E 18 ARG cc_start: 0.7565 (tpp80) cc_final: 0.7147 (tpt-90) REVERT: E 43 LYS cc_start: 0.8465 (mppt) cc_final: 0.8163 (mmtp) REVERT: E 87 ARG cc_start: 0.7017 (mtm-85) cc_final: 0.6406 (ptt-90) REVERT: R 125 THR cc_start: 0.8743 (OUTLIER) cc_final: 0.8529 (t) REVERT: R 249 MET cc_start: 0.8075 (tpp) cc_final: 0.7819 (tpp) REVERT: R 315 PHE cc_start: 0.7633 (t80) cc_final: 0.7302 (t80) REVERT: R 317 LYS cc_start: 0.4999 (mttt) cc_final: 0.4461 (mtmm) outliers start: 25 outliers final: 19 residues processed: 156 average time/residue: 2.1828 time to fit residues: 372.6481 Evaluate side-chains 149 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 274 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 108 optimal weight: 0.3980 chunk 51 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN R 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.134700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.105284 restraints weight = 38907.982| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.13 r_work: 0.3279 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.6401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9045 Z= 0.148 Angle : 0.536 7.814 12277 Z= 0.284 Chirality : 0.043 0.432 1397 Planarity : 0.005 0.055 1557 Dihedral : 4.470 42.535 1242 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.63 % Allowed : 21.32 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.26), residues: 1122 helix: 2.85 (0.25), residues: 387 sheet: 0.14 (0.32), residues: 260 loop : -0.32 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 211 HIS 0.005 0.001 HIS B 230 PHE 0.015 0.001 PHE R 287 TYR 0.010 0.001 TYR R 204 ARG 0.007 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 449) hydrogen bonds : angle 4.56147 ( 1278) SS BOND : bond 0.01247 ( 4) SS BOND : angle 1.09276 ( 8) covalent geometry : bond 0.00334 ( 9041) covalent geometry : angle 0.53561 (12269) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14297.97 seconds wall clock time: 244 minutes 33.46 seconds (14673.46 seconds total)